R/combinations.R

In laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

`combinations` <-
function(n, r, v = 1:n, set = TRUE, repeats.allowed=FALSE)
{
  if(mode(n) != "numeric" || length(n) != 1
     || n < 1 || (n %% 1) != 0) stop("bad value of n")
  if(mode(r) != "numeric" || length(r) != 1
     || r < 1 || (r %% 1) != 0) stop("bad value of r")
  if(!is.atomic(v) || length(v) < n)
    stop("v is either non-atomic or too short")
  if( (r > n) & repeats.allowed==FALSE)
    stop("r > n and repeats.allowed=FALSE")
  if(set) {
    v <- unique(sort(v))
    if (length(v) < n) stop("too few different elements")
  }
  v0 <- vector(mode(v), 0)
  ## Inner workhorse
  if(repeats.allowed)
    sub <- function(n, r, v)
      {
        if(r == 0) v0 else
        if(r == 1) matrix(v, n, 1) else
        if(n == 1) matrix(v, 1, r) else
        rbind( cbind(v[1], Recall(n, r-1, v)),
              Recall(n-1, r, v[-1]))
      }
  else
    sub <- function(n, r, v)
      {
        if(r == 0) v0 else
        if(r == 1) matrix(v, n, 1) else
        if(r == n) matrix(v, 1, n) else
        rbind(cbind(v[1], Recall(n-1, r-1, v[-1])),
              Recall(n-1, r, v[-1]))
      }
  sub(n, r, v[1:n])
}